Model and report changes

1. The model now accounts for the ongoing immunisation programme, stratifying the population of people still susceptible to infection with the virus according to their immunisation status (unimmunised/1 dose/2 doses). We use data on the daily proportions of the population getting immunised to inform this splitting of the population, assuming that it takes three weeks for vaccine-derived immunity to develop. Vaccine efficacy is assumed against both infection and death, using values for the efficacy in agreement with those found here. We have a changepoint in the vaccine efficacy on the 10th May, which marks a transition from alpha being the dominant variant, to delta.
2. The model now also accounts for a different susceptibility to infection in each adult age group (no prior information is used); and for the under-15s, (using prior information from Viner et al, 2020, which estimates children to be less likely to acquire infection when in contact with an infectious individual).
3. The model has the ability to incorporate estimates of community prevalence, by region and age group, from the Office of National Statistics COVID-19 Infection Survey (see Data Sources for details). These are included weekly since the outset of the Survey in May 2020 for the age groups >4 years to inform trends in incidence that are too recent to be captured by the data on deaths.
4. The geographical definition has been changed from the seven NHS regions (map) to the nine regions typically used in government (map). This new spatial definition more appropriately reflects the existing regional heterogeneity.
5. The underlying probability of an unvaccinated individual dying following infection with SARS-CoV2 (the infection-fatality rate, IFR) is allowed to change gradually over the course of 30 days every (approximately) 100 days. This is designed to reflect fluctuations due to seasonal effects, demand on healthcare services or the emergence of new virus variants of differing severity.
6. The ‘Epidemic summary’ now only reports the current value for the IFR by age. To visualise how this has changed over time in our model, see the IFR tab in the ‘Infections and Deaths’ section of the report. The quantity that is now plotted under this tab is the probability of dying if infected, taking into account the impact of the immunisation programme.

Updated findings

1. The estimate of the daily number of new infections on the 19th June across England is 15,200 (11,600–19,000, 95% credible interval). Though incidence is still increasing, this represents a slight downward revision of our most recent published estimate of 11th June.
2. The daily infection rate is estimated to be the highest in the North West (NW) and the North East (NE) with 42 infections per 100K population per day. These correspond to 3,040 and 1,100 new daily infections respectively. The South West (SW) is the third highest with 32 infections per 100k (1,790 daily infections) followed by the West Midlands (WM) (26 per 100,000 and 1,510 new infections every day). All other regions now have more than 10 new infections per 100k population, with incidence in the South East (SE) still the lowest (18 per 100k). Note that a substantial proportion of these daily infections will be asymptomatic.
3. We predict that the number of deaths occurring daily is likely to remain low but also likely to start increasing. For the 10th July we forecast between 32 and 79 daily deaths, though there is a distinct lack of fit to these data over the past two months with consequent very low confidence in these projections.
4. The probability of Rt exceeding 1 is 95% in the NW, 75% in the SW and 68% in the SE. It is greater than 50% in each of NE, WM and in London (GL). This probability is lowest for the East Midlands, where it is only 31%.
5. The growth rate for England has decreased to 0.01 (0.00–0.02, 95% credible interval) per day. This means that, nationally, the number of infections is highly likely to be increasing, although there is considerable uncertainty and heterogeneity across regions, with possible negative growth in some regions. This rate of growth corresponds to a doubling in the number of new infections every 78.9 days
6. London, followed by the NE and the West Midlands (WM), has the highest attack rates, that is the proportions of the regional populations who have ever been infected, with 32%, 28% and 26% respectively. The SW continues to have the lowest attack rate at 15%. These attack rates are entirely consistent with our previous published report.
7. Note that the deaths data used are only very weakly informative on Rt over the last two weeks and are thankfully sparse. Therefore, the estimate for current incidence, Rt and the forecast of daily numbers of deaths are likely to be subject to some revision.

Interpretation

The plots of the estimated Rt over the most recent weeks show that the Rt appear to have peaked three weeks ago and have declined slightly since then, in the absence of any further major relaxation of pandemic mitigation measures. The NW had the highest peak in Rt of 1.36 (CrI 1.15–1.57) with a subsequent fall to 1.14 (0.97–1.30). Current levels of incidence were last seen during the growing phase of the pandemic at the very end of September and will, consequently, require careful monitoring.

From the end of March onwards, the incidence of deaths has continued to fall more sharply than predicted by the model, which is now suggesting a gradual rise over the coming few weeks. This implies that the ONS estimates and the data on deaths are giving conflicting signals and, while this lack of fit has been reduced this week, further model development is required to try and address this discrepancy.

The greatest impact of the changed assumptions regarding the efficacy of the vaccines is in the estimated age-specific probabilities of death given infection (infection fatality rate, IFR). Corresponding plots now show a sharper decline in the IFR once the immunisation programme begins to have an impact in late January. From the end of January we estimate a decreasing IFR in all adult age groups, but most steeply in the older ages. This drop measures the benefits of immunisation against death over and above the benefits against infection. Specifically, there is an estimated fall to a still-high 2.1% in the over-75s and 0.08% overall. The overall impact of the immunisation programme can be seen more clearly in the ‘All Ages’ plot, where the precipitous decline in IFR since late January is a product of this efficacy against death but also of the increasing proportion of infections in young people; older age groups are immunised and become protected against infection. The impact of the second immunisation doses in the 25-44 age-group is beginning to become apparent with a fall after an initial plateau.

For context, alongside the data used here, other indicators (e.g. hospital admissions, reported new positive tests) are suggesting a resurgent epidemic, largely due to the increasing dominance and spread of the Delta strain. Prevalence of infection, as estimated by the ONS Coronavirus Infections Survey, is close to 0.20% in England, though there is large regional heterogeneity with a plateau and perhaps even a slight downturn in many regions. Again, as we consider the possible lifting of social-distancing measures with an Rt around 1, there is the potential for the epidemic to display a range of qualitative behaviours over the coming period. The next few weeks will be crucial. We will continue to monitor the situation closely.